Contacts of the helix formed by residues 356 - 369 (chain D) in PDB entry 1F9Q
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLN 356 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317D SER* 3.8 21.2 + - - -
354D ASP* 2.7 42.1 + - - +
355D LEU* 1.3 73.0 - - - +
357D ALA* 1.3 65.4 + - - +
358D PRO* 3.2 24.3 - - + -
359D LEU* 4.0 20.2 - - + +
360D TYR* 3.0 19.7 + - - +
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Residues in contact with ALA 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355D LEU 3.7 1.2 + - - -
356D GLN* 1.3 70.3 - - - +
358D PRO* 1.3 75.5 - - + +
360D TYR* 3.2 23.0 - - + +
361D LYS* 2.9 42.1 + - + +
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Residues in contact with PRO 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356D GLN* 3.1 20.9 - - + -
357D ALA* 1.3 99.5 - - + +
359D LEU* 1.3 66.7 + - + +
361D LYS* 3.9 0.6 - - - -
362D LYS* 2.9 33.2 + - - +
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Residues in contact with LEU 359 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316D THR 4.4 4.7 - - - +
317D SER* 4.0 34.1 - - - +
319D VAL* 3.8 35.4 - - + +
321D PRO* 5.3 4.7 - - + -
353D LEU* 4.7 12.8 - - + -
354D ASP 5.2 3.8 - - - +
356D GLN* 3.8 27.9 + - + +
358D PRO* 1.3 79.1 - - + +
360D TYR* 1.3 53.1 + - - +
362D LYS* 3.2 10.3 - - + +
363D ILE* 2.7 51.2 + - + +
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Residues in contact with TYR 360 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264C ILE* 4.1 5.4 - - + -
265C LYS* 4.7 5.5 + - - +
268C LEU* 3.1 42.7 - - + +
327D LEU* 4.9 5.4 - - + -
329D VAL* 6.4 1.1 - - + -
341D LEU* 3.6 30.5 - - + -
353D LEU* 5.4 2.7 - - + -
354D ASP 5.6 0.2 - - - +
355D LEU 4.0 9.4 - - - -
356D GLN 3.0 22.4 + - - -
357D ALA* 3.2 32.3 + - + +
358D PRO 3.3 0.8 - - - -
359D LEU* 1.3 75.8 - - + +
361D LYS* 1.3 78.5 + - + +
362D LYS 2.6 14.7 + - - -
363D ILE* 2.9 8.6 + - - +
364D ILE* 2.7 52.8 + - + +
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Residues in contact with LYS 361 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264C ILE* 6.4 0.2 - - + -
357D ALA* 2.9 34.1 + - + +
358D PRO* 3.9 0.9 - - - +
360D TYR* 1.3 93.1 - - + +
362D LYS* 1.3 57.8 + - - +
364D ILE* 4.2 8.7 - - + +
365D LYS* 3.9 14.8 + - - +
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Residues in contact with LYS 362 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321D PRO* 4.1 24.0 - - + -
358D PRO* 2.9 32.8 + - - +
359D LEU* 3.2 11.0 - - + +
360D TYR 2.6 1.0 + - - -
361D LYS* 1.3 78.1 - - - +
363D ILE* 1.3 65.0 + - - +
364D ILE 3.2 1.1 - - - -
365D LYS* 2.9 19.2 + - + +
366D LYS* 3.1 12.1 + - - +
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Residues in contact with ILE 363 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319D VAL* 4.6 2.7 - - + -
321D PRO* 4.0 22.0 - - + +
324D ILE* 3.3 38.6 - - + -
327D LEU* 4.3 12.3 - - + -
353D LEU* 3.3 29.8 - - + -
359D LEU* 2.7 39.6 + - + +
360D TYR* 2.9 4.7 + - - +
362D LYS* 1.3 72.0 - - - +
364D ILE* 1.3 63.6 + - - +
366D LYS* 3.2 7.9 + - - +
367D LEU* 3.0 41.7 + - + +
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Residues in contact with ILE 364 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229C VAL* 4.8 13.7 - - + -
260C TYR* 5.6 0.7 - - + -
264C ILE* 3.2 35.0 - - + -
327D LEU* 4.0 19.3 - - + -
329D VAL* 5.6 3.8 - - + -
360D TYR* 2.7 42.1 + - + +
361D LYS* 4.3 8.5 - - + +
363D ILE* 1.3 73.2 - - - +
365D LYS* 1.3 53.6 + - - +
367D LEU* 3.9 6.1 - - - +
368D LEU* 2.6 70.4 + - + +
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Residues in contact with LYS 365 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361D LYS 3.9 13.0 + - - +
362D LYS* 2.9 15.0 + - + +
364D ILE* 1.3 77.5 - - - +
366D LYS* 1.3 68.5 + - - +
368D LEU* 4.4 2.2 - - - -
369D GLU* 2.9 69.2 + - - +
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Residues in contact with LYS 366 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231C LYS* 3.8 24.0 - - - +
321D PRO* 4.0 37.0 - - + +
322D ARG* 3.6 32.5 - - + +
362D LYS* 3.1 8.2 + - + +
363D ILE 3.6 7.4 - - - +
365D LYS* 1.3 79.5 - - - +
367D LEU* 1.3 59.5 + - + +
369D GLU* 4.6 0.7 - - - -
370D SER* 3.4 21.9 + - - -
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Residues in contact with LEU 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229C VAL* 3.7 34.5 - - + +
231C LYS* 3.4 28.8 - - + +
239C ALA* 3.1 16.3 - - - +
321D PRO 5.0 4.0 - - - +
324D ILE* 3.2 31.2 - - + +
325D THR 4.5 1.1 - - - -
326D SER 4.5 3.1 - - - -
327D LEU* 3.9 25.1 - - + +
363D ILE* 3.0 29.5 + - + +
364D ILE* 3.9 3.4 - - - +
366D LYS* 1.3 79.2 - - + +
368D LEU* 1.3 61.1 + - - +
369D GLU 3.3 2.2 - - - -
370D SER* 2.9 21.2 + - - -
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Residues in contact with LEU 368 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229C VAL* 3.3 31.4 - - + -
239C ALA* 4.2 10.7 - - + +
241C LEU* 3.5 21.3 - - + -
255C LEU* 3.6 23.0 - - + +
260C TYR* 3.2 37.0 - - + +
364D ILE* 2.6 38.9 + - + +
365D LYS* 4.1 3.6 - - - +
367D LEU* 1.3 73.9 - - - +
369D GLU* 1.3 63.5 + - + +
370D SER 3.4 1.8 + - - +
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Residues in contact with GLU 369 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365D LYS* 2.9 59.4 + - + +
366D LYS* 4.6 1.6 - - - -
368D LEU* 1.3 82.6 - - + +
370D SER* 1.3 62.9 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il